Tue Oct 11 08:33:44 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Oct 11 2011 at 08:33:44 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 333 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2017 !!! WARNING: HIR 40 has a net charge of 0.5140 !!! WARNING: SEP 177 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.7054394 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): 10.97400 53.18200 ymin,ymax (A): 6.592000 48.09800 zmin,zma (A): 21.32700 71.79200 x,y,z range (A): 42.20800 41.50600 50.46500 scale (grids/A): 0.7054394 object centre (A): 32.07800 27.34500 46.55950 number of atom coordinates read : 2017 total number of charged atoms : 1990 net assigned charge : 6.039011 assigned positive charge : 327.0220 centred at (gu) : 91.01746 90.79343 90.39831 assigned negative charge : -320.9830 centred at (gu) : 91.12000 90.91627 90.47801 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6984 nv = 96 ne = 84 npr = 38425 no. pairs analyzed = 38425 no. exposed pairs = 2511 no. arc points = 17422 no. surface atoms = 860 nbur = 1157 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 480 mr = 4026 m= 2 mr = 81 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3359 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1709 ## 156 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7982 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.1725496E-08 1.1527545E-08 midg,1,midg; midg,igrid,midg 9.3268014E-08 -1.2859982E-08 1,midg,midg; igrid,midg,midg 8.1460385E-08 -1.2501004E-09 gauss-seidel spectral radius is 0.9895219 estimated iterations to convergence 80 setup time was (sec) 0.5400000 now iterating at: 08:33:45 rms-change max change #iterations 0.2067690 34.75206 at 10iterations 2.5324134E-02 3.739334 at 20iterations 3.1950625E-03 0.4060364 at 30iterations 4.6011436E-04 6.5885544E-02 at 40iterations 9.7071585E-05 1.4706612E-02 at 50iterations finished qdiffx linear iterations at : 08:33:49 total time elapsed so far: 3.810000 # loops : 50 mean,max change (kT/e) : 9.7071585E-05 1.4706612E-02 energy calculations done at 3.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.990000 DelPhi exited at 08:33:49 3.996u 0.267s 0:04.85 87.6% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Oct 11 2011 at 08:33:49 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 333 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2017 !!! WARNING: HIR 40 has a net charge of 0.5140 !!! WARNING: SEP 177 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.116318 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): 10.97400 53.18200 ymin,ymax (A): 6.592000 48.09800 zmin,zma (A): 21.32700 71.79200 x,y,z range (A): 42.20800 41.50600 50.46500 scale (grids/A): 2.116318 object centre (A): 32.07800 27.34500 46.55950 number of atom coordinates read : 2017 total number of charged atoms : 1990 net assigned charge : 6.039011 assigned positive charge : 327.0220 centred at (gu) : 93.05237 92.38023 91.19478 assigned negative charge : -320.9830 centred at (gu) : 93.36018 92.74870 91.43398 start vw surface at 0.1400000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 73879 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17422 grid for indexing accessible points = 1.400000 m= 30835 mr = 52563 m= 6026 mr = 23490 m= 522 mr = 3995 m= 13 mr = 261 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6800000 number of dielectric boundary points 30966 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 73 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 15806 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.7054394 object centre at (A) : 32.07800 27.34500 46.55950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.0243992E-02 2.3703797E-02 midg,1,midg; midg,igrid,midg 2.5001600E-02 6.9637308E-03 1,midg,midg; igrid,midg,midg 4.0518094E-02 -3.7737907E-04 gauss-seidel spectral radius is 0.9988226 estimated iterations to convergence 231 setup time was (sec) 0.9800000 now iterating at: 08:33:51 rms-change max change #iterations 4.704513 206.3587 at 10iterations 2.324574 71.90556 at 20iterations 1.150029 32.65514 at 30iterations 0.5710154 17.61567 at 40iterations 0.2831360 9.197877 at 50iterations 0.1401246 4.209701 at 60iterations 6.9278084E-02 2.417955 at 70iterations 3.4267213E-02 0.9962626 at 80iterations 1.7004307E-02 0.5042682 at 90iterations 8.4307734E-03 0.2561315 at 100iterations 4.1958373E-03 0.1280661 at 110iterations 2.1168070E-03 5.9490204E-02 at 120iterations finished qdiffx linear iterations at : 08:33:59 total time elapsed so far: 9.270000 # loops : 120 mean,max change (kT/e) : 2.1168070E-03 5.9490204E-02 energy calculations done at 9.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.450000 DelPhi exited at 08:34:00 9.450u 0.290s 0:10.46 93.1% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Oct 11 2011 at 08:34:00 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 333 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2017 !!! WARNING: HIR 40 has a net charge of 0.5140 !!! WARNING: SEP 177 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.174477 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): 10.97400 53.18200 ymin,ymax (A): 6.592000 48.09800 zmin,zma (A): 21.32700 71.79200 x,y,z range (A): 42.20800 41.50600 50.46500 scale (grids/A): 3.174477 object centre (A): 32.07800 27.34500 46.55950 number of atom coordinates read : 2017 total number of charged atoms : 1990 net assigned charge : 6.039011 assigned positive charge : 327.0220 centred at (gu) : 94.57855 93.57037 91.79214 assigned negative charge : -320.9830 centred at (gu) : 95.04020 94.12319 92.15102 start vw surface at 0.1400000 fill in re-entrant regions at 0.9600000 boundary points on vw surface= 170154 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17422 grid for indexing accessible points = 1.400000 m= 94579 mr = 126112 m= 39223 mr = 78938 m= 11405 mr = 32424 m= 2122 mr = 8740 m= 256 mr = 1554 m= 2 mr = 155 m= 0 mr = 0 time to grow re-entrant surface = 1.120000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.180000 number of dielectric boundary points 69818 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.320000 number of grid points assigned charge 15920 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 2.116318 object centre at (A) : 32.07800 27.34500 46.55950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6137466 0.1951614 midg,1,midg; midg,igrid,midg 0.1800036 0.1175419 1,midg,midg; igrid,midg,midg 0.4004566 -1.5994571E-02 gauss-seidel spectral radius is 0.9992967 estimated iterations to convergence 297 setup time was (sec) 2.490000 now iterating at: 08:34:03 rms-change max change #iterations 10.48315 363.0117 at 10iterations 6.200568 149.9494 at 20iterations 3.653238 81.84038 at 30iterations 2.155077 43.21605 at 40iterations 1.262453 22.32686 at 50iterations 0.7403507 14.05860 at 60iterations 0.4352285 7.272156 at 70iterations 0.2545505 4.768293 at 80iterations 0.1488255 2.648682 at 90iterations 8.7092072E-02 1.654480 at 100iterations 5.1049698E-02 0.8861661 at 110iterations 2.9864468E-02 0.6256733 at 120iterations 1.7560937E-02 0.3103409 at 130iterations 1.0340151E-02 0.1905174 at 140iterations 6.1632069E-03 0.1163044 at 150iterations 3.7243925E-03 6.5208435E-02 at 160iterations 2.3190479E-03 4.1938782E-02 at 170iterations 1.5049168E-03 2.7786255E-02 at 180iterations finished qdiffx linear iterations at : 08:34:16 total time elapsed so far: 16.16000 # loops : 180 mean,max change (kT/e) : 1.5049168E-03 2.7786255E-02 energy calculations done at 16.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.34000 DelPhi exited at 08:34:17 16.337u 0.338s 0:17.42 95.6% 0+0k 0+0io 0pf+0w